cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i Sig_18_Blood.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_2.tnseq.vcf.gz --algo OrientationBias --tumor_sample Sig_18_Blood negative_somatic_control_2.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample Sig_18_Blood --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_2.tnseq.segments negative_somatic_control_2.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113710154, elapsed 0.7s, est remaining 12.6s, peak mem 145MB, user 6.7s, sys 0.4s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.5s, peak mem 145MB, user 13.1s, sys 0.8s, output queue size 6
progress 15% @chr2:178606921, elapsed 1.9s, est remaining 11.0s, peak mem 146MB, user 19.7s, sys 1.2s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.5s, est remaining 10.1s, peak mem 147MB, user 25.6s, sys 1.7s, output queue size 0
progress 25% @chr4:70530939, elapsed 3.2s, est remaining 9.5s, peak mem 148MB, user 32.2s, sys 2.2s, output queue size 9
progress 30% @chr5:135873921, elapsed 3.8s, est remaining 9.0s, peak mem 150MB, user 39.1s, sys 2.6s, output queue size 4
progress 35% @chr6:104849042, elapsed 4.4s, est remaining 8.2s, peak mem 152MB, user 45.1s, sys 3.0s, output queue size 3
progress 40% @chr7:106872437, elapsed 5.1s, est remaining 7.6s, peak mem 153MB, user 51.9s, sys 3.4s, output queue size 2
progress 45% @chr8:143835562, elapsed 5.7s, est remaining 7.0s, peak mem 154MB, user 58.6s, sys 3.8s, output queue size 0
progress 50% @chr10:21726144, elapsed 6.4s, est remaining 6.4s, peak mem 155MB, user 65.1s, sys 4.2s, output queue size 1
progress 55% @chr11:34132025, elapsed 7.0s, est remaining 5.7s, peak mem 155MB, user 71.5s, sys 4.6s, output queue size 1
progress 60% @chr12:12718707, elapsed 7.6s, est remaining 5.1s, peak mem 155MB, user 77.7s, sys 5.0s, output queue size 8
progress 65% @chr13:32149648, elapsed 8.2s, est remaining 4.4s, peak mem 155MB, user 84.3s, sys 5.4s, output queue size 6
progress 70% @chr15:35538174, elapsed 8.8s, est remaining 3.8s, peak mem 155MB, user 90.6s, sys 5.7s, output queue size 8
progress 75% @chr16:28494582, elapsed 9.5s, est remaining 3.2s, peak mem 156MB, user 97.0s, sys 6.1s, output queue size 0
progress 80% @chr17:40034816, elapsed 10.1s, est remaining 2.5s, peak mem 156MB, user 104.1s, sys 6.5s, output queue size 2
progress 85% @chr19:1805788, elapsed 10.8s, est remaining 1.9s, peak mem 157MB, user 110.8s, sys 6.9s, output queue size 3
progress 90% @chr19:54630974, elapsed 11.4s, est remaining 1.3s, peak mem 158MB, user 117.4s, sys 7.2s, output queue size 2
progress 95% @chr22:31944634, elapsed 12.9s, est remaining 0.7s, peak mem 344MB, user 132.1s, sys 7.7s, output queue size 10
progress 100% @chrY:23180126, elapsed 13.5s, est remaining 0.0s, peak mem 344MB, user 138.1s, sys 8.1s, output queue size 440
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 74586807
output file size: 51111
reads: 1501816
contig: 178193 intervals 76355618 bases
"assemble": 189 calls 0.427 user 0.000 sys 0.437 real
"assemble_addRead": 189 calls 0.000 user 0.000 sys 0.007 real
"assemble_buildGraph": 446 calls 0.196 user 0.000 sys 0.189 real
"assemble_computecigar": 274 calls 0.090 user 0.000 sys 0.066 real
"assemble_kg_build_calcsize": 446 calls 0.070 user 0.000 sys 0.100 real
"assemble_kg_build_clear": 608 calls 0.030 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 892 calls 0.093 user 0.000 sys 0.092 real
"assemble_kg_build_threading": 284 calls 0.096 user 0.000 sys 0.085 real
"assemble_kg_op1": 284 calls 0.040 user 0.000 sys 0.063 real
"assemble_kg_op2": 284 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 284 calls 0.010 user 0.000 sys 0.005 real
"assemble_sg_clean": 274 calls 0.000 user 0.000 sys 0.020 real
"assemble_sg_create": 274 calls 0.038 user 0.000 sys 0.031 real
"checkGraph": 189 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 189 calls 0.090 user 0.000 sys 0.069 real
advance: 189104 calls 14.835 user 0.311 sys 18.507 real
assemble_region: 189 calls 0.517 user 0.000 sys 0.515 real
build_pileup: 70986 calls 0.369 user 0.023 sys 0.456 real
build_stats: 71708 calls 2.154 user 0.071 sys 2.187 real
build_variants: 158 calls 0.000 user 0.000 sys 0.001 real
calc: 128714 calls 2.346 user 0.048 sys 2.858 real
calc_region: 158 calls 1.667 user 0.002 sys 1.839 real
call_region: 158 calls 0.022 user 0.000 sys 0.041 real
clip_region: 347 calls 0.030 user 0.000 sys 0.033 real
done: 1 calls 0.428 user 0.001 sys 0.433 real
execute: 1 calls 0.006 user 0.001 sys 13.487 real
fetch: 743546 calls 0.654 user 0.073 sys 0.821 real
fetch_ref: 745694 calls 1.621 user 0.526 sys 2.732 real
fetch_region: 189 calls 0.000 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 43.904 user 0.912 sys 55.314 real
idle: 35 calls 0.004 user 0.011 sys 12.817 real
init: 1 calls 0.050 user 0.010 sys 0.058 real
pairhmm: 454 calls 2.803 user 0.020 sys 2.957 real
realign: 158 calls 0.428 user 0.000 sys 0.431 real
region: 367297 calls 2.205 user 0.041 sys 2.457 real
tracker: 367297 calls 0.345 user 0.091 sys 0.533 real
trim_region: 189 calls 0.000 user 0.000 sys 0.001 real
overall: 361123840 mem 153.794 user 10.816 sys 14.782 real